Updating to 2023.10 version and dispersion

Author: daavid00

README.md

@@ -1,5 +1,5 @@
 [![Build Status](https://github.com/OPM/pyopmspe11/actions/workflows/CI.yml/badge.svg)](https://github.com/OPM/pyopmspe11/actions/workflows/CI.yml)
-<a href="https://www.python.org/"><img src="https://img.shields.io/badge/python-3.8%20|%203.9%20|%203.10-blue.svg"></a>
+<a href="https://www.python.org/"><img src="https://img.shields.io/badge/python-3.8%20|%203.9%20|%203.10%20|%203.11-blue.svg"></a>
 [![Code style](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/ambv/black)
 [![License: MIT](https://img.shields.io/badge/license-MIT-blue)](https://opensource.org/license/mit/)
 
@@ -12,7 +12,7 @@ Here we use the [_OPM-Flow_](https://opm-project.org/?page_id=19) simulator.
 
 ## Installation
 You will first need to install
-* Flow (https://opm-project.org)
+* Flow (https://opm-project.org, Release 2023.10 or current master branches)
 
 To build dune and the corresponding OPM master branches from source (e.g., you are a macOS user), you can run the script
 `./build_dune_and_opm-flow.bash`, which in turn should build flow in the folder 

docs/_images/dissolved.png

@@ -38,14 +38,14 @@ The following input lines in the configuration file are:
     12                #If cartesian, number of z cells [-]; if tensor, variable array of z-refinment; if corner-point, fix array of z-refinment (17 entries)
     70. 36.25         #Temperature bottom and top rig [C]            
     19620000.         #Pressure on the top [Pa]
-    1e-9 2e-8         #CO2 diffusion (in liquid and gas) [m^2/s]
+    1e-9 2e-8 0       #Diffusion (in liquid and gas) [m^2/s] and dispersion [m] (disperison only available in Flow master)
     8.5e-1 2500.      #Rock specific heat and density (for spe11b/c)
     5e4 1.            #Pore volume on lateral boundaries and width of buffer cell [m] (for spe11b/c)
     150. 10.          #Elevation of the parabola and back [m] (for spe11c) 
 
-In line 5 you specify if you are using OPM Flow from the master branch or from the latest stable release (OPM-flow 2023.4 release).
-This since there are continuous changues in the OPM master branch (e.g., the format of the boundary condition keyword BC). Then we 
-will keep updating the decks for using Flow from master and also we will keep the framework to produce decks compatible for the latest OPM stable release .
+In line 5 you specify if you are using OPM Flow from the master branch or from the latest stable release (OPM-flow 2023.10 release).
+This since there are continuous changues in the OPM master branch (e.g., implementation of mechanical dispersion). Then we 
+will keep updating the decks for using Flow from master and also we will keep the framework to produce decks compatible for the latest OPM stable release.
 The immiscible model allows for faster prototyping while the complete model includes dissolution of the components in the
 gas and liquid phases, in addition to thermal effects. Regarding the grid type, the cartesian mode generates an uniform grid
 with the defined number of elements in lines 9 to 11. The tensor grid allows to define arrays in each direction where the grid
@@ -63,6 +63,10 @@ resulting in 17 levels. Then, the z-refinment in each of these levels is set. Se
     elements, the tensor grid by setting the x-array to 50,100,20; the y-array to 5,10,70,10,5; and the z-array to 5,10,20,20,20,20,20,5; and 
     the corner-point grid using the same xy-arrays as in the tensor grid and for the z-refinment 4,4,3,3,5,3,7,5,13,5,7,5,3,9,21,21,2. 
 
+.. warning::
+    Dispersion seems to work fine for the spe11a case where there are no thermal effects nor water evaporation. However, for spe11b/c there are
+    issues with the current implementation (we are working in this, then for now disperison should be set to 0 for spe11b/c).  
+
 ***********************
 Soil-related parameters
 ***********************
@@ -96,13 +100,17 @@ The following entries define the properties of the different facies:
     PERM4 506.625 PORO4 0.20 THCONR4 1.25
     PERM5 1013.25 PORO5 0.25 THCONR5 0.92
     PERM6 2026.50 PORO6 0.35 THCONR6 0.26
-    PERM7       0 PORO7    0 THCONR7 2.00
+    PERM7       0 PORO7 1E-6 THCONR7 2.00
 
 .. figure:: figs/kr.png
 .. figure:: figs/cap.png
 
     Visualization in ResInsight of the relative permeability and capillary pressure functions in the facie 1.
 
+.. note::
+    For spe11b/c, adding a small value of porosity in facie 7 (i.e., 1E-6 in this example), allows to include the termal effects
+    from the caprock (facie 7).
+
 ***********************
 Well-related parameters
 ***********************

docs/_images/facies.png

@@ -11,8 +11,7 @@ The numerical simulations for the CO2 are performed using the
 Concept
 -------
 Simplified and flexible testing framework for the three cases in the SPE Comparative Solution Project
-using the open-source simulator OPM Flow. This is work in progress and current efforts focus on the
-implementation of dispersion. 
+using the open-source simulator OPM Flow. 
 
 Overview
 --------

docs/_images/saturation.png

@@ -14,4 +14,8 @@ The simulation results are saved in the **flow** folder, and
 In addition, some figures are plotted in png format in the **figures** folder.
 Then after running **pyopmspe11**, one could modify the generated OPM related files and 
 run directly the simulations calling the Flow solvers, e.g., to add tracers 
-(see the OPM Flow documentation `here <https://opm-project.org/?page_id=955>`_). 
+(see the OPM Flow documentation `here <https://opm-project.org/?page_id=955>`_).
+
+.. tip::
+    If you install the dev-requirements.txt, executing **pytest --cov=pyopmspe11 --cov-report term-missing tests/** runs the
+    configuration files in the tests with different argument options for **pyopmspe11**, then one can see the different outputs.

docs/_sources/configuration_file.rst.txt

@@ -110,15 +110,15 @@ <h2>Reservoir-related parameters<a class="headerlink" href="#reservoir-related-p
 <span class="linenos">11</span><span class="mi">12</span>                <span class="c1">#If cartesian, number of z cells [-]; if tensor, variable array of z-refinment; if corner-point, fix array of z-refinment (17 entries)</span>
 <span class="linenos">12</span><span class="mf">70.</span> <span class="mf">36.25</span>         <span class="c1">#Temperature bottom and top rig [C]</span>
 <span class="linenos">13</span><span class="mf">19620000.</span>         <span class="c1">#Pressure on the top [Pa]</span>
-<span class="linenos">14</span><span class="mf">1e-9</span> <span class="mf">2e-8</span>         <span class="c1">#CO2 diffusion (in liquid and gas) [m^2/s]</span>
+<span class="linenos">14</span><span class="mf">1e-9</span> <span class="mf">2e-8</span> <span class="mi">0</span>       <span class="c1">#Diffusion (in liquid and gas) [m^2/s] and dispersion [m] (disperison only available in Flow master)</span>
 <span class="linenos">15</span><span class="mf">8.5e-1</span> <span class="mf">2500.</span>      <span class="c1">#Rock specific heat and density (for spe11b/c)</span>
 <span class="linenos">16</span><span class="mf">5e4</span> <span class="mf">1.</span>            <span class="c1">#Pore volume on lateral boundaries and width of buffer cell [m] (for spe11b/c)</span>
 <span class="linenos">17</span><span class="mf">150.</span> <span class="mf">10.</span>          <span class="c1">#Elevation of the parabola and back [m] (for spe11c)</span>
 </pre></div>
 </div>
-<p>In line 5 you specify if you are using OPM Flow from the master branch or from the latest stable release (OPM-flow 2023.4 release).
-This since there are continuous changues in the OPM master branch (e.g., the format of the boundary condition keyword BC). Then we
-will keep updating the decks for using Flow from master and also we will keep the framework to produce decks compatible for the latest OPM stable release .
+<p>In line 5 you specify if you are using OPM Flow from the master branch or from the latest stable release (OPM-flow 2023.10 release).
+This since there are continuous changues in the OPM master branch (e.g., implementation of mechanical dispersion). Then we
+will keep updating the decks for using Flow from master and also we will keep the framework to produce decks compatible for the latest OPM stable release.
 The immiscible model allows for faster prototyping while the complete model includes dissolution of the components in the
 gas and liquid phases, in addition to thermal effects. Regarding the grid type, the cartesian mode generates an uniform grid
 with the defined number of elements in lines 9 to 11. The tensor grid allows to define arrays in each direction where the grid
@@ -141,6 +141,11 @@ <h2>Reservoir-related parameters<a class="headerlink" href="#reservoir-related-p
 the corner-point grid using the same xy-arrays as in the tensor grid and for the z-refinment 4,4,3,3,5,3,7,5,13,5,7,5,3,9,21,21,2.</span><a class="headerlink" href="#id1" title="Link to this image"></a></p>
 </figcaption>
 </figure>
+<div class="admonition warning">
+<p class="admonition-title">Warning</p>
+<p>Dispersion seems to work fine for the spe11a case where there are no thermal effects nor water evaporation. However, for spe11b/c there are
+issues with the current implementation (we are working in this, then for now disperison should be set to 0 for spe11b/c).</p>
+</div>
 </section>
 <section id="soil-related-parameters">
 <h2>Soil-related parameters<a class="headerlink" href="#soil-related-parameters" title="Link to this heading"></a></h2>
@@ -169,7 +174,7 @@ <h2>Soil-related parameters<a class="headerlink" href="#soil-related-parameters"
 <span class="linenos">40</span><span class="n">PERM4</span> <span class="mf">506.625</span> <span class="n">PORO4</span> <span class="mf">0.20</span> <span class="n">THCONR4</span> <span class="mf">1.25</span>
 <span class="linenos">41</span><span class="n">PERM5</span> <span class="mf">1013.25</span> <span class="n">PORO5</span> <span class="mf">0.25</span> <span class="n">THCONR5</span> <span class="mf">0.92</span>
 <span class="linenos">42</span><span class="n">PERM6</span> <span class="mf">2026.50</span> <span class="n">PORO6</span> <span class="mf">0.35</span> <span class="n">THCONR6</span> <span class="mf">0.26</span>
-<span class="linenos">43</span><span class="n">PERM7</span>       <span class="mi">0</span> <span class="n">PORO7</span>    <span class="mi">0</span> <span class="n">THCONR7</span> <span class="mf">2.00</span>
+<span class="linenos">43</span><span class="n">PERM7</span>       <span class="mi">0</span> <span class="n">PORO7</span> <span class="mf">1E-6</span> <span class="n">THCONR7</span> <span class="mf">2.00</span>
 </pre></div>
 </div>
 <figure class="align-default">
@@ -181,6 +186,11 @@ <h2>Soil-related parameters<a class="headerlink" href="#soil-related-parameters"
 <p><span class="caption-text">Visualization in ResInsight of the relative permeability and capillary pressure functions in the facie 1.</span><a class="headerlink" href="#id2" title="Link to this image"></a></p>
 </figcaption>
 </figure>
+<div class="admonition note">
+<p class="admonition-title">Note</p>
+<p>For spe11b/c, adding a small value of porosity in facie 7 (i.e., 1E-6 in this example), allows to include the termal effects
+from the caprock (facie 7).</p>
+</div>
 </section>
 <section id="well-related-parameters">
 <h2>Well-related parameters<a class="headerlink" href="#well-related-parameters" title="Link to this heading"></a></h2>

docs/_sources/introduction.rst.txt

@@ -91,8 +91,7 @@ <h1>Introduction<a class="headerlink" href="#introduction" title="Link to this h
 <section id="concept">
 <h2>Concept<a class="headerlink" href="#concept" title="Link to this heading"></a></h2>
 <p>Simplified and flexible testing framework for the three cases in the SPE Comparative Solution Project
-using the open-source simulator OPM Flow. This is work in progress and current efforts focus on the
-implementation of dispersion.</p>
+using the open-source simulator OPM Flow.</p>
 </section>
 <section id="overview">
 <h2>Overview<a class="headerlink" href="#overview" title="Link to this heading"></a></h2>

docs/_sources/output_folder.rst.txt

@@ -93,6 +93,11 @@ <h1>Output folder<a class="headerlink" href="#output-folder" title="Link to this
 Then after running <strong>pyopmspe11</strong>, one could modify the generated OPM related files and
 run directly the simulations calling the Flow solvers, e.g., to add tracers
 (see the OPM Flow documentation <a class="reference external" href="https://opm-project.org/?page_id=955">here</a>).</p>
+<div class="admonition tip">
+<p class="admonition-title">Tip</p>
+<p>If you install the dev-requirements.txt, executing <strong>pytest –cov=pyopmspe11 –cov-report term-missing tests/</strong> runs the
+configuration files in the tests with different argument options for <strong>pyopmspe11</strong>, then one can see the different outputs.</p>
+</div>
 </section>
 
 

docs/configuration_file.html

@@ -44,21 +44,11 @@
   </form>
 </div>
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
-              <ul class="current">
+              <ul>
 <li class="toctree-l1"><a class="reference internal" href="introduction.html">Introduction</a></li>
 <li class="toctree-l1"><a class="reference internal" href="configuration_file.html">Configuration file</a></li>
 <li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</a></li>
-<li class="toctree-l1 current"><a class="reference internal" href="api.html">pyopmspe11 Python API</a><ul class="current">
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 </ul>

docs/introduction.html

@@ -44,21 +44,11 @@
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 </div>
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
-              <ul class="current">
+              <ul>
 <li class="toctree-l1"><a class="reference internal" href="introduction.html">Introduction</a></li>
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 <li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</a></li>
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